Gut Microbiome, Soil Microbiome: Different Ecosystems, Same Principles
Soil Health is the New Root to Holistic Health
The soil microbiome is composed mostly of Actinomycetota, Acidobacteriota, Pseudomonadota (adding to about 50%), followed by Verrucomicrobiota, Chloroflexota, Bacteroidota, and a lot more. The human gut microbiome on its side is composed of 90% of Bacillota and Bacteroidota (Firmicutes and Bacteroidetes) followed by a little of Actinobacteria and Proteobacteria (Banerjee et al., 2023). The compositional setup and the metabolic reactions these microbes perform are not the same. Yet, there are many similarities in the way humans and plants rely on our symbiosis with our microbes for nutrition, defense against pathogens, resilience, and overall health. Here are some of the governing principles.
Born in Symbiosis
Animal life was born in a microbial world about 430 million years ago (Garwood and Edgecombe, 2011). The coexistence with microbes drove the evolution of the digestive tube. Our genomes don’t code for sufficient enzymes to go through all the energy in our food, this is why towards the end of the digestive tract the microbial population increases and makes the most of leftovers, for the benefit of colon cells that grab the waste as their principal energy source.
Similarly, algae moved from oceans to terrestrial grounds roughly 400 million years ago, before soil even existed — indeed, plants were needed for the creation of humus. They only could do the trip because of an association with fungi, which enabled them to retrieve mineral nutrition from rocks and reach out further to find water sources.
Animals and plants had previously developed symbiosis in their core when their cells evolved from englobing microbial cells, which later became mitochondria, the energy factory of the Eukaryotic cell, and chloroplasts, the locus of photosynthesis in plants. More about the endosymbiotic theory and the importance of Lynn Margulis in the evolution of symbiosis in this previous blog and this one.
We Invest in Nourishing the Microbiome
So far, wherever we looked for symbiosis between microbes and host, we found it. Ed Yong’s I Contain Multitudes is a great testimony of this richness. The author looks at many transmission strategies for the microbiome legacy from one generation to the next, in particular among insects. Covering the eggs with a microbe-rich gelly the larvae eat when they hatch. Sealing off the burrow with a paste that the wasp larvae must nibble before making their way into the world, etc.
In humans, seeding microbial friends is mostly taken care of during birth through the vaginal canal. Children born by C-section have a different microbiota set up in the first few months, and it is thought that exposing the newborn to the mother’s vaginal secretions can help mature a healthier microbiome.
Then, mothers invest about 30% of the energy supply in their breast milk to build Human Milk Oligosaccharides (HMOs) that their babies can’t absorb… Scientists scratched their heads when they made this discovery, thinking nature wouldn’t maintain such a wasteful system. Yet it was not wasteful: HMOs are an investment to build partnerships deep inside. To feed our second genome. All through our lives, we are encouraged to eat our fruits and vegetables, and a good part of their health benefits is mediated through the microbiome.
It is the same for plants: 30–40% of their photosynthesis products are channeled into the soil through their root exudates: almost all plants invest in their community of microbes and fungi that prolong their root, reach much farther for food, complete their capabilities with externalized enzymes that can make available minerals that would otherwise be out of reach, phosphorous especially (The Hidden Half of Nature, L’Origine du Monde). Estimates reckon that the food plants get from fungi in exchange represents 90% of their biomass. And beyond the crucial help their root microbiota provides for nutrition, it’s also a very important front of protection.
“When you team with microbes, you feed them, and they feed the roots.” — Lowenfels and Lewis in Teaming with Microbes.
The Microbiome, the First Line of Defense
The gut and root microbiomes act as the first line of defense against infection. Mechanisms of protection include pathogen barrier, immune stimulation, and nutrition absorption.
An example of direct defense is the case of Arthrobotrys dactyloides, referred by Marc-André Selosse in L’Origine du Monde and by Teaming with Microbes. This fungus deploys hyphae that present a peculiarity: they burst to three times their volume in an instant upon touch. This trick traps nematodes, soil worms that can be pathogenic for the plants, that get stuck in the nodes, and soon become digested by the fungus. Other fungi produce toxic compounds that immobilize nematodes, also allowing time for the hyphae to grow into it and digest the prey.
Part of the defense is, very much like what happens in the gut, competition with pathogens. If sufficient microbial richness is in the spot, the disease-causing agents don’t have a chance to settle or find food.
Another mechanism of protection is through direct antagonism (when the microbial symbionts produce antibiotics) and I should remind you that most of today’s antibiotic toolbox comes from soil microbes.
Besides, as everything is linked, supporting the plants’ nutritional profile is supporting the plant’s immune system function — just like with us humans, when microbes help us get our vitamins! In What Your Food Ate, Bigle and Montgomery describe many studies showing that regenerative agriculture, based on practices that nurture soil life and symbioses with soil microbes and fungi, leads to increased contents in many substances that are the plant’s secondary metabolites — the plant’s immune system. Importantly, being able to produce these compounds because they have access to the right micro-nutrition and oligo elements means they are much more resistant to disease and pests (cf. John Kempf’s Regenerative Agriculture podcast), and they are also more healthful for human consumption, as these very compounds also present antioxidant properties and protective effects against aging and cancer.
In this previous blog about Plants and their Microbes inspired from Jamais Seul by Selosse, I referred to 4 major functions for which plants rely on their symbionts: nutrition, immune defenses, protection, and development.
Diversity is Protective
It is still difficult to define a healthy gut microbiome, today in 2023. Yet, what scientists agree upon is that diversity is associated with health and resilience, while a loss of microbial richness can imply a loss of functions, and open the door to disease. The most well-known case of diversity loss causing severe disease is the case of C. difficile outgrowth after an antibiotic treatment, leading to acute diarrhea that can be lethal. The best treatment so far against resistant Cdiff infection? Fecal Microbiota Transplant (FMT), which restores biodiversity.
Disease-suppressive soils is an expression you hear a lot when listening to John Kempf’s podcast Regenerative Agriculture. What is special about these soils? They host a wide diversity of life. And as explained above, this means a pest is almost always kept in control by its predator, and can’t outgrow competition. Pests are not fully eliminated but are kept in control. Having a little bit of pests in the field can even be positive in keeping the plant’s immune system alert, which also enriches it with the good phytochemical substances we discussed above like polyphenols, lycopene, etc., that serve as antioxidants and prebiotics. Similarly with Cdiff, when a disease outbreaks in the field, one solution can be the pendant of FMT for the soil, or Actively Aerated Compost Tea (AACT) which offers the plant and soil a good microbial diversity. More on AACT in the Teaming With Microbes’s Digest here.
“Soils with a high diversity of bacterial types are more likely to have a large number of nonpathogenic bacteria outcompeting pathogenic bacteria for space and nutrients.” — Jeff Lowenfels & Wayne Lewis in Teaming with Microbes.
Microbial Richness is Similar in a Healthy Gut and Healthy Soil
The concentration of microbes in the soil of a garden, prairie, or forest ranges between 100 million to 1 billion bacteria per teaspoon (or per gram) (The Hidden Half of Nature, Teaming with Microbes). This is a little less than what is found in the lower gut, but overall not far off from the bacterial concentration in the gut (from 10 thousand in the jejunum, to 10 million in the ileum up to 1 trillion in the colon, Dieterich et al., 2018).
What this says is bacterial presence and abundance play a key role in both ecosystems. Although they don’t play the same partition of metabolisms, the soil acts as a reservoir of microbes for the plant, which can then be transferred to the animal — including humans — eating the plant (Soil Microbiomes and One Health, Banerjee et al., 2023). In consequence, soil richness could contribute to a diverse gut microbiome.
Modernity’s Attacks on Diversity
Martin Blaser was the pioneer in identifying the risks caused by antibiotics and the modern way of life impacts on microbial diversity, and how this loss affects human health, in Missing Microbes, 2014.
If the overuse of antibiotics fueled our gut microbiota dysbiosis and civilization diseases, in parallel tillage, fertilizers, and pesticides led to missing microbes in agricultural soils and to the same type of dysbiosis in plants. (cf. Regenerative Agriculture, and Teaming with microbes that advocate never to use fertilizers above NPK 10:10:10).
Because we can’t see microbes, we have underestimated for all of humans’ history their key roles in ecosystems. Both the gut and soil microbiomes can be considered virtual, forgotten organs. We were born and evolved in a microbial world, and so were plants. We grew to be way more collaborative than we would have ever thought. And in the past century, our diet, medical practices, and agricultural practices all decimated this cooperative biodiversity inside and outside of us.
“Most life on Earth is invisible to us.” — Bikle and Montgomery in The Hidden Half of Nature.
When speaking about antibiotics and pesticides, Montgomery says:
“We have chiseled away the foundations on which we stand.” — Montgomery in The Hidden Half of Nature.
Of Probiotics and PGPR specificity
Probiotics’ benefits are mostly strain-specific: not all L. acidophilus will deliver the same benefits, and when choosing a probiotic, you should pick one that has demonstrated benefits at this dose.
Some functions, however, are shared among a species or even beyond. This is why the European Food Safety Authority declared itself in favor of a claim for L. bulgaricus and St. thermophilus — all strains of these species— to support lactose digestion. Indeed, they produce lactase, thus degrade lactose, detoxifying it for people who lack the enzyme.
Similarly, Plant Growth Promoting Rhizobacteria (PGPR) and mycorrhizae can be more or less specific to a function and a host. Endophytes, like Trichoderma species, can enhance plant growth. According to Jeff Lowenfels and Wayne Lewis, Trichoderma T-22 can reduce the nitrogen need of corn by 30 to 40, while the strain PTA-3710 is a nematode inhibitor, and T-39 lives off gray mold Botrytis cinerea, and others oppose other pathogens.
Some mycorrhizae are very specific and will form endomycorrhizae with only one kind of plant, but commercially-available ectomycorrhizal fungi & arbuscular mycorrhizae (EM and AM mixes) contain generalist species that can link with many kinds of plants — helping them absorb over half a plant’s nitrogen needs, and as much as 80% of their phosphorous uptake.
We Have Power in Restoring Symbiosis
The world of the microbiome is building awareness that our genome explains only a part of our individuality and potential. Our second genome completes this genetic makeup, and we have the power to nurture it and promote its diversity and resilience, by increasing our food sources diversity, our plants and fiber intake, reducing our consumption of processed foods that include preservatives, improving our exposure to nature and soil, and being physically active.
The soil has gone through the same trauma as we people since the 50s, with increased use of tillage, pesticides, and concentrated fertilizers, damaging microbes and fungal communities much needed for plants' health and growth. Yet, there are alternative practices that can be followed: these are the practices promoted in regenerative agriculture: no-till, cover crops, and culture rotation. They can also be enhanced by the application of microbial mixes, from commercial sources, or Actively Aerated Compost Teas for instance. Understanding soil ecology and the specific symbioses of the different plant types with different microbes and ratios of fungi vs bacteria is important to offer each plant the right balance of microbes, pH, and nutrition they need.
This is so true that the FAO has released an article and policymaker executive summary titled The Soil Microbiome A Game Changer for Food and Agriculture.
And as everything is linked, restoring soil symbioses will also help nurture our health, because foods produced in healthy soils are richer in micronutrients that contribute to the diversity in our gut microbiota and protect from oxidation, inflammation, and cancer (What Your Food Ate).
“It’s such a collaborative place, inside and outside of us.” — Bikle and Montgomery in The Hidden Half of Nature.
